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comparison biobb_solvate.xml @ 2:4c626e984fde draft default tip

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author spanish_national_institue_of_bioinformatics
date Fri, 12 Apr 2019 07:18:48 -0400
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1:21a0f28aea68 2:4c626e984fde
1 <tool id="biobb_solvate" name="Solvate" version="0.1.5">
2 <description>: creates a Gromacs topology file adding solvent molecules to a given input. </description>
3 <requirements>
4 <requirement type="binary">docker</requirement>
5 </requirements>
6 <command detect_errors="aggressive">
7 ln -f -s ${inputname} ${inputname}.${inputname.ext};
8 ln -f -s ${inputzip} ${inputzip}.${inputzip.ext};
9 #if $config.sele == "option1":
10 ln -s -f ${config.properties} ${config.properties}.${config.properties.ext};
11 #end if
12 docker run -v $__root_dir__/database/files:$__root_dir__/database/files quay.io/biocontainers/biobb_md:0.1.5--py_0 solvate --input_solute_gro_path $inputname.${inputname.ext} --input_top_zip_path ${inputzip}.${inputzip.ext}
13 #if $config.sele == "option1":
14 --config ${config.properties}.${config.properties.ext}
15 #else if $config.sele == "option2":
16 --config ${config.jsonstr}
17 #end if
18 --output_gro_path $__root_dir__/database/files/000/$outname
19 --output_top_zip_path $outputzip;
20 #if $config.sele == "option1":
21 rm -f ${config.properties}.${config.properties.ext};
22 #end if
23 rm -f ${inputname}.${inputname.ext} ${inputzip}.${inputzip.ext};
24 mv $__root_dir__/database/files/000/$outname $output
25 </command>
26 <inputs>
27 <param name="outname" type="text" value="mySolvate.gro" label="Output GRO name" help="Name for the Output GRO. Format: [output].gro "/>
28 <param name="outnamezip" type="text" value="solvate.zip" label="Output ZIP name" help="Name for the Output topology in ZIP. Format: [output].zip "/>
29 <param name="inputname" type="data" format="gro" label="Input GRO file" help="Select your input GRO file. Format: [input].gro"/>
30 <param name="inputzip" type="data" format="zip" label="Topology file" help="Select your input TOP topology ZIP. Format: [input].zip"/>
31 <conditional name="config">
32 <param name="sele" type="select" label="Take tool settings:" help="Select where tool settings are to be read from">
33 <option value="option1">from configuration file</option>
34 <option value="option2">from JSON string</option>
35 <option value="option3" selected="true">by default</option>
36 </param>
37 <when value="option1">
38 <param name="properties" type="data" format="yml,json" optional="false" label="Configuration file" help="File containing tool settings. See below for the syntax"/>
39 </when>
40 <when value="option2">
41 <param name="jsonstr" type="text" value="{}" optional="false" label="JSON string" help="JSON string containing tool settings. See below for the syntax"/>
42 </when>
43 <when value="option3">
44 </when>
45
46 </conditional>
47 </inputs>
48 <outputs>
49 <data name="output" format="gro" label="${outname}"/>
50 <data name="outputzip" format="zip" label="${outnamezip}"/>
51
52 </outputs>
53 <tests>
54 <test>
55 </test>
56 </tests>
57 <help>
58 .. class:: warningmark
59
60
61 Check the syntax for setting the tool parameters at the original library documentation: https://biobb-md.readthedocs.io/en/latest/gromacs.html#module-gromacs.solvate
62
63 -----
64
65 .. image:: ${static_path}/images/biobb.png
66 :height: 57
67 :width: 150
68
69
70 **https://bioexcel.eu**
71 </help>
72 <citations>
73 <citation type="bibtex">
74 @misc{githubbiobb,
75 author = {Andrio P, Hospital A, Gelpi JL},
76 year = {2019},
77 title = {biobb: BioExcel building blocks },
78 publisher = {GitHub},
79 journal = {GitHub repository},
80 url = {https://github.com/bioexcel/biobb_io},
81 }</citation>
82 </citations>
83 </tool>